This proposal to change .JPG, .Jpg, .jpeg, .JpEg etc all to .jpg for new uploads has been accepted. The same for .tiff, .tif, .TIF etc to .tif. For all other extensions, none should have uppercase characters anymore.
When a user tries to upload a file with (for example) a .JPG extension, the extension should be changed to .jpg, preferably in silence. The file upload should not be denied.
If possible (I don't know how complicated this would be), it would also be nice if a message like "File extension automatically changed from JPEG to jpg" could be appended to the upload/edit comment. No showstopper if this is not possible, but it would be nice.
See Also:
T36703: Normalize file extension while uploading file in UploadWizard (only concerns UploadWizard)
T34660: File extensions for the same file type should not allow variations of a file name (File:X.jpg, File:X.jpeg, File:X.JPG should all refer to the same file) (only appears to concern enwiki)
T42326: File extension letter case treatment should be unified on Commons (closed because T36703 was closed)
T31284: Upload form should change file extensions to the canonical form automatically (lowercase, jpeg→jpg etc.)
T213484: Normalize file extensions (capital vs small letters; jpg vs jpeg) for new uploads on Commons
T144593: File extension changes automatically while moving ogg audio file on Commons, caused by a gadget
T42479: File extensions should be automatically decided by MIME type at upload